A portable capillary waveguide biosensor platform has been developed for both the detection and quantification of target DNA molecules using in situ hybridization, with application to detecting marine bacteria from natural samples. While fluorescence based techniques enable very low detection of target molecules, they typically lack the necessary control of experimental and molecular factors that are essential for absolute concentration measurements. A novel dual detector approach circumvents these limitations by providing for instantaneous normalization of the fluorescence intensity. Detection limits of 30 pg/ml of Alexa A-532-S dye complex have been achieved. The probe sequence DNA, attached to the interior surface of the capillary, can be denatured for repetitive use of the capillary. Design guidelines for an optimal CWB, togteher with results using synthetic targets, will be presented.